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Hi, Did you use nanopre ONT data as a .fastq? Thanks
./minimap2 -ax map-ont reference.fasta BC10.fastq -o output.sam
Is reference.fasta file an assembled genome? Do you know how to further use .sam file after mapping the data on ONT?
Hi David, Thank you so much for sending the code. It is really great. It gives really beautiful synteny plot. I am very happy that I can make different color...
I tried both ways: minimap2 -c ref-genome.fasta assembly-contigs.fasta -o output.paf minimap2 -a ref-genome.fasta assembly-contigs.fasta -o output.sam
Thanks alot!!! I will try with those options suggested by you.
Thank you Mahul. what is the default values for 'M' and 'N' I do not see this information in the notes?
Thank you. I really appreciate it. Now I got it. -l and -ml are the options for the this.
thanks
Hi Mahul, four files were generate after finishing the process. aln_summary_prefix.tsv param_summary_prefix.txt anchor_summary_prefix.txt merged_prefix.fasta However, I have an issue - hifi-hybrid.fasta - before assembly - 11,626 fasta sequences after quickmerge...